* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/elfgen.Rcheck’ * using R Under development (unstable) (2024-02-02 r85853) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘elfgen/DESCRIPTION’ ... OK * this is package ‘elfgen’ version ‘2.3.3’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘elfgen’ can be installed ... [18s/18s] OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [24s/25s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking examples with --run-donttest ... [55s/200s] ERROR Running examples in ‘elfgen-Ex.R’ failed The error most likely occurred in: > ### Name: elfchange > ### Title: Plot percent richness change for various percent flow reductions > ### Aliases: elfchange > > ### ** Examples > > ## No test: > # We don't run this example by R CMD check, because it takes >10s > > # Generate plot of percent richness change for various percent flow reductions > watershed.df <- elfdata(watershed.code = '0208020104', ichthy.localpath = tempdir()) Ichthy dataset previously downloaded Processing NHD features: 81 NHD features found containing richness data Processing NHD feature mean annual flow: Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Request failed [502]. Retrying in 1 seconds... Request failed [502]. Retrying in 1.5 seconds... Error in out[[1]] : subscript out of bounds Calls: elfdata -> -> query_usgs_geoserver Spherical geometry (s2) switched on Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [7s/21s] [7s/22s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(elfgen) > > test_check("elfgen") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-elfdata.R:37:13'): Function returns a dataframe ──────────────── Error in `out[[1]]`: subscript out of bounds Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-elfdata.R:37:13 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::is.data.frame(...) 5. └─elfgen::elfdata(watershed.code = test.ichthy.dataframe, ichthy.localpath = tempdir()) 6. └─nhdplusTools::get_nhdplus(comid = COMID) 7. └─nhdplusTools:::query_usgs_geoserver(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ] Error: Test failures Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs See ‘/data/blackswan/ripley/R/packages/tests-devel/elfgen.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:12.30, 191.12 + 17.52